* installing *source* package ‘goldfish’ ...
** package ‘goldfish’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 accepts -g... yes
checking how to run the C++ preprocessor... /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether /usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 accepts -g... (cached) yes
checking for macOS... not found as on Linux
checking for OpenMP... R was not built as a library
missing
configure: creating ./config.status
config.status: creating src/Makevars
--------------------------------------------------
Configuration for goldfish version
================
openMP: -DARMA_DONT_USE_OPENMP
cxxflags: -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3
libs:
--------------------------------------------------
** libs
using C++ compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/goldfish/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c DyNAM_MM_default.cpp -o DyNAM_MM_default.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c DyNAM_choice_default.cpp -o DyNAM_choice_default.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c DyNAM_rate_default.cpp -o DyNAM_rate_default.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c DyNAM_rate_ordered_default.cpp -o DyNAM_rate_ordered_default.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c REM_default.cpp -o REM_default.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c REM_ordered_default.cpp -o REM_ordered_default.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c compute_coordination_selection.cpp -o compute_coordination_selection.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c compute_multinomial_selection.cpp -o compute_multinomial_selection.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c compute_poisson_selection.cpp -o compute_poisson_selection.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c convert_rdata_to_cdata.cpp -o convert_rdata_to_cdata.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c gather_progress.cpp -o gather_progress.o
compute_poisson_selection.cpp:42:9: warning: variable 'id_dep_event' set but not used [-Wunused-but-set-variable]
42 | int id_dep_event = 0;
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c gather_receiver_model.cpp -o gather_receiver_model.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c gather_sender_model.cpp -o gather_sender_model.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -I../inst/include -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -I'/data/gannet/ripley/R/test-clang/RcppArmadillo/include' -isystem /usr/local/clang19/include -I/usr/local/clang/include -DARMA_DONT_USE_OPENMP -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c gather_sender_receiver_model.cpp -o gather_sender_receiver_model.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o goldfish.so DyNAM_MM_default.o DyNAM_choice_default.o DyNAM_rate_default.o DyNAM_rate_ordered_default.o REM_default.o REM_ordered_default.o RcppExports.o compute_coordination_selection.o compute_multinomial_selection.o compute_poisson_selection.o convert_rdata_to_cdata.o gather_progress.o gather_receiver_model.o gather_sender_model.o gather_sender_receiver_model.o -DARMA_DONT_USE_OPENMP -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/goldfish/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/goldfish/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/goldfish/src'
installing to /data/gannet/ripley/R/packages/tests-clang/goldfish.Rcheck/00LOCK-goldfish/00new/goldfish/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (goldfish)